There are some variability in USB3 enclosure performance and USB3 won't let you use TRIM and update SSD firmware. USB3 has an adverse affect on latency.
I have an early 2014 15in rMBP and Blackmagic gives me the following:
USB3 ($50 startech with USAP): 150 MBps write, 290 MBps read
Thunderbolt (OWC): 365 MBps write, 380 MBps read
Internal PCE: 975 MBps write, 996 MBps read
Two decent performing rotational drives in a RAID0 striped configuration in a thunderbolt enclosure provides 330 MBps read and write performance along with 4TB of storage.
For reference, a typical USB2.0 portable drive may reach 30 MBps on a good day.
Whether it makes any difference for one's specific use case, I dunno. There is more to it than just comparing benchmarks.